title: Molecular dynamics simulations of certain mutant peptide models from staphylococcal nuclease reveal that initial hydrophobic collapse associated with turn propensity drives β-hairpin folding.
abstract: An important nucleation event during the folding of staphylococcal nuclease involves the formation of a β-hairpin by the sequence (21) DTVKLMYKGQPMTFR(35) . Earlier studies show that the turn sequence 'YKGQP' has an important role in the folding of this β-hairpin. To understand the active or passive nature of the turn sequence 'YKGQP' in the folding of the aforementioned β-hairpin sequence, we studied glycine mutant peptides Ac-(2) DTVKLMYGGQPMTFR(16) -NMe (K9G:15), Ac-(2) DTVKLMYKGGPMTFR(16) -NMe (Q11G:15), Ac-(2) DTVKLMYGGGPMTFR(16) -NMe (K9G/Q11G:15), and Ac-(2) DTVKLMGGGGGMTFR(16) -NMe (penta-G:15) by using molecular dynamics simulations, starting with two different unfolded states, polyproline II and extended conformational forms. Further, 5mer mutant turn peptides Ac-(2) YGGQP(6) -NMe (K3G:5), Ac-(2) YKGGP(6) -NMe (Q5G:5), Ac-(2) YGGGP(6) -NMe (K3G/Q5G:5), and Ac-(2) GGGGG(6) -NMe (penta-G:5) were also studied individually. Our results show that an initial hydrophobic collapse and loop closure occurs in all 15mer mutants, but only K9G:15 mutant forms a stable native-like β-hairpin. In the other 15mer mutants, the hydrophobic collapsed state would not proceed to β-hairpin formation. Of the different simulations performed for the penta-G:15 mutant, in only one simulation a nonnative β-hairpin conformation is sampled with highly flexible loop region ((8) GGGGG(12) ), which has no specific conformational preference as a 5mer. While the sequence 'YGGQP' in the K3G:5 simulation shows relatively higher β-turn propensity, the presence of this sequence in K9G:15 peptide seems to be driving the β-hairpin formation. Thus, these results seem to suggest that for the formation of a stable β-hairpin, the initial hydrophobic collapse is to be assisted by a turn propensity. Initial hydrophobic collapse alone is not sufficient to guide β-hairpin formation.
authors.affiliation: Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
authors.forename: Rashmi Tambe
authors.initials: RT
authors.lastname: Shukla
authors.forename: Naveen
authors.initials: N
authors.lastname: Kumar
authors.forename: Yellamraju U
authors.initials: YU
authors.lastname: Sasidhar
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008836:Micrococcal Nuclease / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D008836:Micrococcal Nuclease
keywords: glycine mutants; hydrophobic collapse; molecular dynamics simulation; protein folding; β-hairpin; β-turn